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1609 materials found

Hands-on for 'Upload data to Galaxy' tutorial

The questions this addresses are:
- How to upload data to Galaxy

The objectives are:
- Learn how to upload a file by pasting in a URL
- Learn how to import data from a shared library
- Determine the best strategy to get data into Galaxy

Keywords: introduction

Resource type: hands-on tutorial

Hands-on for 'Design and plan session, course, materials' tutorial

The questions this addresses are:
- Is the structured approach to course design?
- How to articulate learning outcomes commensurate with the cognitive complexity of the target learning?
- How to devise learning experiences and course content?
- What are the steps that can help trainers...

Keywords: contributing

Resource type: hands-on tutorial

Hands-on for 'Principles of learning and how they apply to training and teaching' tutorial

The questions this addresses are:
- What are the main principles that drive learning?
- How can these principles be applied to training and teaching?

The objectives are:
- Describe how learning works according to a few learning models
- Explain how learning models can help you improve your...

Keywords: contributing

Resource type: hands-on tutorial

Slides for 'Overview of the Galaxy Training Material for Instructors' tutorial

The questions this addresses are:
- How can I use the GTN for teaching?
- What resources are available?
- Why is it a good choice?

Keywords: teaching

Resource type: slides

3DBionotes COVID-19 Structural Hub: A Central Resource for Validation Information and Refined Models

Poster presented at the 21st European Conference on Computational Biology (ECCB 2022), celebrated in Sitges, Spain, 12-21 September 2022.

Scientific topics: Structural biology, Data visualisation, Data integration and warehousing, Data mining

Keywords: covid-19, Structural biology, Protein models, electron microscopy, data annotation, Web Services (5596), Quality Validation, Cryo-Electron Microscopy

Resource type: Poster

Hands-on for 'Deploying Tailscale/Headscale for private mesh networking' tutorial

The questions this addresses are:
- What is Tailscale?
- When is it useful?
- Is it right for me?

The objectives are:
- Setup a tailnet across a few nodes

Keywords: admin, wireguard, networking

Resource type: hands-on tutorial

Hands-on for 'Deploying Wireguard for private mesh networking' tutorial

The questions this addresses are:
- What is wireguard?
- When is it useful?
- Is it right for me?

The objectives are:
- Setup a wireguard mesh across a few nodes

Keywords: admin, wireguard, networking

Resource type: hands-on tutorial

Intermediate Research Software Development Skills In Python

This is a multi-day, intermediate-level lesson/course in software development skills for researchers using Python as a programming language. A typical learner for this course may be someone who is working in academic research and, needing to write some code, has gained basic software development...

Keywords: intermediate, Coding, software engineering, Carpentries Incubator

Organisation and utilisation of hologenomic datasets – course notes

This course covered the generation and application of large-scale holo-omic data sets, such as those produced within the HoloFood project. This course was run in September 2022, in-person in Bilbao, as part of the 1st Applied Hologenomics Conference. These course notes include the lecture slides...

Scientific topics: Metatranscriptomics, Sample collections, Metabolomics, Metagenomics

Keywords: hologenomics, metagenomics, Metabolomics, MGnify, Workshop

Resource type: Slides, course materials, hands-on tutorial

WEBINAR: Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud

This record includes training materials associated with the Australian BioCommons webinar ‘Portable, reproducible and scalable bioinformatics workflows using Nextflow and Pawsey Nimbus Cloud’. This webinar took place on 20 September 2022.

Event description 

Bioinformatics workflows can...

Keywords: Bioinformatics, Workflows, Nextflow, Containerisation

bio-tools - EDAM drop-in hackathon - discussions

bio.tools, EDAM drop-in hackathon and discussions

Data clearinghouse, validation and curation of BioSamples - ENA - Breeding API endpoints - MAR databases

 

Data clearinghouse, validation and curation of BioSamples/ENA/Breeding API endpoints/MAR databases
 

Prototyping the new PSICQUIC 2-0

 

Prototyping the new PSICQUIC 2.0
 

Spatial Omics Data Analysis

This is an international course hosted by the National Bioinformatics Infrastructure Sweden (ELIXIR-SE) in collaboration with the Human Developmental Cell Atlas (HDCA), the Royal Institute of Technology, Stockholm University, Karolinska Institutet, Uppsala University, Charité Clinical University...

Keywords: spatial, Multiomics, In situ sequencing, Spatial Transcriptomics, Single cell RNAseq

Resource type: FREE online course, course materials, online course

WORKSHOP: Single cell RNAseq analysis in R

This record includes training materials associated with the Australian BioCommons workshop ‘Single cell RNAseq analysis in R’. This workshop took place over two, 3.5 hour sessions on 22 and 3 August 2022.

Event description

  • Analysis and interpretation of single cell RNAseq (scRNAseq) data...

Keywords: Bioinformatics, Analysis, Transcriptomics, R software, Single cell RNAseq, scRNAseq

FAIR principles in practice for health data

FAIR principles in practice for health data was developed in the context of the Swiss Personalized Health Network (SPHN) initiative and is part of a series of trainings centered around the [SPHN Interoperability...

Scientific topics: Computer science, Data management, FAIR data, Medical informatics

Operations: Standardisation and normalisation, Design

Keywords: Clinical data, RDF, Knowledge graph, Semantic framework, FAIR, Findability, Accessibility, Interoperability, Reusability

Resource type: Video, E-learning

Hands-on for 'Combining datasets after pre-processing' tutorial

The questions this addresses are:
- I have some AnnData files from different samples that I want to combine into a single file. How can I combine these and label them within the object?

The objectives are:
- Combine data matrices from different samples in the same experiment
- Label the...

Scientific topics: Transcriptomics

Keywords: single-cell, single-cell, 10x, paper-replication, español, transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Inferring Trajectories using Python (Jupyter Notebook) in Galaxy' tutorial

The questions this addresses are:
- How can I infer lineage relationships between single cells based on their RNA, without a time series?

The objectives are:
- Execute multiple plotting methods designed to maintain lineage relationships between cells
- Interpret these plots

Scientific topics: Transcriptomics

Keywords: single-cell, single-cell, 10x, paper-replication, interactive-tools, transcriptomics

Resource type: hands-on tutorial

Hands-on for 'Comparative gene analysis in unannotated genomes' tutorial

The questions this addresses are:
- I have several genomes assemblies that are not annoatated (or I do not trust annotations)
- I am interested to compare structure of a particular gene across these genome assemblies
- How do I do that?

The objectives are:
- Provide a quick method for...

Keywords: genome-annotation, evolution, annotation, vgp, cookbook, eukaryote, prokaryote

Resource type: hands-on tutorial

WEBINAR: Getting started with whole genome mapping and variant calling on the command line

This record includes training materials associated with the Australian BioCommons webinar ‘Getting started with whole genome mapping and variant calling on the command line’. This webinar took place on 24 August 2022.

Event description 

Life scientists are increasingly using whole genome...

Keywords: Genome mapping, Variant calling, Bioinformatics, Workflows

Exploring structural and functional annotations of IDPs with DisProt

In this course you will learn how to explore a DisProt entry, along with its main features (structural and functional annotations). You will also learn how to search the database for specific annotated aspects and how to download the output of a search.

Keywords: Curation, Databases, Ontologies, Intrinsically disordered proteins, Protein sequence analysis, Protein function analysis

Resource type: Webinar, Training materials

Getting Started With BioMedIT

No description provided.

SPARQL endpoints at BiGCaT

Lecture discussing the SPARQL endpoints provided by the Maastricht Universty Dept. of Bioinformatics, BiGCaT.

Keywords: WikiPathways, AOP-Wiki, ChEMBL, SPARQL, chemistry, cheminformatics

SPARQLing Biology: a Beginners Course

The workshop was covering the whole range of Semantic Approaches developed and used at the Department of Bioinformatics at Maastricht University (BiGCaT). The setting was alternating between introductory presentations and hands on exercises starting with more general questions like “what is a...

Keywords: SPARQL, RDF, biology, ontology

Hands-on for 'Genome Assembly Quality Control' tutorial

The questions this addresses are:
- Is my genome assembly ready for annotation and/or scaffolding?

The objectives are:
- Assess assembly quality

Keywords: assembly, assembly, quality control

Resource type: hands-on tutorial

Slides for 'Genome assembly quality control.' tutorial

The questions this addresses are:
- Assembly: Is my genome assembly ready for scaffolding?
- Annotation: Is my genome assembly ready for structural annotation?

Keywords: assembly

Resource type: slides

WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software

This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022.

Event description 

bio.tools provides easy...

Keywords: Bioinformatics, Research software, EDAM, Workflows, FAIR

Hands-on for 'Refining Genome Annotations with Apollo (eukaryotes)' tutorial

The questions this addresses are:
- How to visualize your genome after automated annotations have been performed?
- How to manually annotate genome after automated annotations have been performed?
- How to evaluate and visualize annotated genomic features?
- How do I collaborate when doing...

Keywords: genome-annotation, eukaryote, cyoa

Resource type: hands-on tutorial

An introduction to DisProt

In this course you will learn what type of information is stored in DisProt, gold standard resource of manually curated Intrinsically Disordered Proteins (IDPs) and Intrinsically Disordered Regions (IDRs) from the literature. You will explore the main features of the database, its entries and...

Keywords: Curation, Databases, Ontologies, Intrinsically disordered proteins, Protein sequence analysis, Protein function analysis

Resource type: Webinar, Training materials

WEBINAR: bio.tools - making it easier to find, understand and cite biological tools and software

This record includes training materials associated with the Australian BioCommons webinar ‘bio.tools - making it easier to find, understand and cite biological tools and software’. This webinar took place on 21 June 2022.

Event description

bio.tools provides easy access to essential...

Scientific topics: Workflows, Ontology and terminology

Keywords: Bioinformatics, Research software, EDAM, Workflows, FAIR